Package: limma

Version: 3.9.2

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch limma_3.9.2.tar.gz

StartedAt: 2011-05-09 15:22:23 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 15:24:56 -0700 (Mon, 09 May 2011)

EllapsedTime: 152.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: limma.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/limma.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limma/DESCRIPTION’ ... OK
* this is package ‘limma’ version ‘3.9.2’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘limma’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'plotMDS'
  ‘xlab’ ‘ylab’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
‘library’ or ‘require’ call not declared from: ‘sma’
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... NOTE
‘library’ or ‘require’ call not declared from: ‘marray’
* checking tests ...
  Running ‘limma-Tests.R’
  Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...920,921c920,921
< mu+alpha    0.3333333 3.333333e-01  5.551115e-17
< mu+beta    -0.3333333 5.551115e-17  3.333333e-01
---
> mu+alpha    0.3333333 3.333333e-01  9.280771e-17
> mu+beta    -0.3333333 9.280771e-17  3.333333e-01
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/Users/biocbuild/bbs-2.9-bioc/meat/limma.Rcheck/00check.log’
for details

* installing *source* package ‘limma’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -c normexp.c -o normexp.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o limma.so normexp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/limma.Rcheck/limma/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘limma.Rnw’ 
** testing if installed package can be loaded

* DONE (limma)

name	user	system	elapsed
LargeDataObject	0.000	0.000	0.001
PrintLayout	0.001	0.001	0.001
TestResults	0	0	0
alias2Symbol	3.712	0.159	4.155
arrayWeights	0.009	0.001	0.011
arrayWeightsQuick	0	0	0
asMatrixWeights	0.002	0.000	0.001
auROC	0.001	0.001	0.002
avearrays	0.002	0.000	0.003
avereps	0.002	0.001	0.002
backgroundcorrect	0.014	0.001	0.015
blockDiag	0.002	0.001	0.002
cbind	0.025	0.001	0.033
channel2M	0.002	0.000	0.002
classifytests	0.003	0.001	0.004
contrasts.fit	0.036	0.002	0.038
controlStatus	0.024	0.001	0.025
convest	2.619	0.019	2.846
dim	0.002	0.000	0.003
dupcor	0.000	0.001	0.000
ebayes	0.015	0.000	0.015
genas	0.133	0.003	0.136
geneSetTest	0.009	0.001	0.008
getSpacing	0.001	0.000	0.001
getlayout	0.001	0.000	0.000
heatdiagram	0.006	0.001	0.007
helpMethods	0	0	0
imageplot	0.048	0.005	0.053
intraspotCorrelation	0.000	0.000	0.001
isfullrank	0.002	0.000	0.002
isnumeric	0.001	0.000	0.002
kooperberg	0	0	0
limmaUsersGuide	0.004	0.002	0.005
lm.series	0	0	0
lmFit	2.169	0.022	2.420
lmscFit	0.013	0.001	0.033
loessfit	0.482	0.004	0.595
ma3x3	0.002	0.001	0.003
makeContrasts	0.001	0.000	0.002
makeunique	0.001	0.001	0.002
merge	0.013	0.001	0.029
mergeScansRG	0	0	0
modelMatrix	0.004	0.000	0.004
modifyWeights	0.001	0.001	0.001
nec	0.001	0.000	0.000
normalizeMedianAbsValues	0.001	0.000	0.001
normalizeRobustSpline	0.004	0.001	0.005
normalizeVSN	0.640	0.032	0.797
normalizebetweenarrays	0.004	0.000	0.004
normalizeprintorder	0	0	0
normexpfit	0.003	0.000	0.003
normexpfitcontrol	0.000	0.000	0.001
normexpfitdetectionp	0.000	0.001	0.001
normexpsignal	0	0	0
plotDensities	0.000	0.001	0.001
plotMDS	0.019	0.003	0.033
plotRLDF	0.555	0.026	0.638
plotma	0.020	0.001	0.020
poolvar	0.001	0.000	0.001
printorder	0.022	0.008	0.031
printtipWeights	0.000	0.001	0.000
propexpr	0	0	0
protectMetachar	0	0	0
qqt	0.003	0.000	0.002
qualwt	0.000	0.000	0.001
read.ilmn	0.000	0.000	0.001
read.maimages	0.001	0.000	0.000
readImaGeneHeader	0.000	0.001	0.000
readgal	0.001	0.000	0.006
removeext	0.000	0.000	0.001
roast	0.069	0.006	0.085
romer	0.628	0.006	0.761
selectmodel	0.039	0.001	0.042
squeezeVar	0.002	0.001	0.002
strsplit2	0.001	0.000	0.001
subsetting	0.007	0.000	0.007
targetsA2C	0.010	0.001	0.010
topRomer	0	0	0
toptable	0.000	0.001	0.001
trigammainverse	0.001	0.000	0.001
trimWhiteSpace	0.001	0.000	0.001
uniquegenelist	0.001	0.000	0.001
unwrapdups	0.001	0.001	0.001
venn	0.058	0.002	0.068
volcanoplot	0	0	0
weightedmedian	0.000	0.000	0.001
zscore	0.001	0.000	0.001